Open a text file and find a motif in the truncated text found inside

motifFinder.pl

#!/usr/bin/perl

use strict;
use warnings;

my $DNAfilename = 'exampleSequence.txt';

unless (open(DNAFILE, $DNAfilename)) {
    print "Could not open file $DNAfilename\n\n";
    exit;
}

my @DNA = <DNAFILE>;
close DNAFILE;

my $DNA = join('',@DNA);

$DNA =~ s/\s//g;

print "Here is the file content:\n", "$DNA\n\n";

my $motif;

do {
    print "Enter a motif to search for: ";
    $motif = <STDIN>;
    chomp $motif;

    if ($DNA =~ /$motif/) {
	print "I found it!\n\n";
    }
    else {
	print "I could not find it.\n\n";
    }
} until ($motif =~ /^\s*$/);

exit;